Abstract The demographic composition of small towns and rural communities in the U.S. has changed dramatically, in part because of the large in-migration of Latino families. For communities to support the health of their members, they must be able to reinforce factors that promote positive youth development (protective factors) and abate factors that hinder it (risk factors). However, much of what is known about risk and resilience comes from research on urban communities. There has been little longitudinal research on Latinos growing up in the rural U.S., and none with sufficient data to understand the etiology of substance use (SU), patterns of health disparities in SU, and factors influencing their health and wellbeing as young adults. We know little about the intersectionality of Latino ethnicity, immigrant status, and rural context and how these relate to the developmental mechanisms of health disparities. This knowledge gap limits prevention and intervention services, as the prevention science paradigm depends on accurately identifying risk and protective factors (RPFs) and developing prevention programs targeting these factors to reduce problem behaviors. The present application capitalizes on existing rich longitudinal data spanning childhood through early adulthood to examine influences on health and well-being of rural Latino youth. Using this existing data, we will examine health disparities in substance use and associated RPFs (a) between 3rd-generation rural Latino and non-Latino White youth, and (b) among rural Latino youth who are 1st-, 2nd- or 3rd-generation immigrants (i.e., children of immigrant or U.S.-born parents). In the supplemental analyses used for triangulation and validation, we will use national cross-sectional data and examine differences in the association between RPFs and alcohol, tobacco, marijuana, and other drug use for Latino youth by the type of residence (rural vs. small and large metro areas) at the historical time points and age ranges corresponding to the longitudinal study. Findings will provide rigorous scientific evidence regarding risk and protective processes for Latino youth in rural areas of the U.S. that may lead to prevention efforts to reduce health disparities in substance use and other health risk behaviors in young adulthood, and potentially reduce disparities in serious illness later in the life course.